Roared to the title by dozens of feverish home fans, the world number three pairing pounced all over the Malaysians from the first point at the Riocentro and never dropped the pressure in the 21-14 21-12 win.
Tontowi and Natsir captured their delegation's first gold of the Rio Games and seventh in Olympic badminton, closing out the match when Goh netted the last shuttlecock.
China's Chen takes badminton title to leave Lee heartbroken again
Malaysia have waited 52 years for an Olympic champion but their hopes of breaking the drought were extinguished in just 44 minutes by the rampant Indonesians.
GB badminton duo Ellis and Langridge bag bronze after beating Chinese pair
Marcus Ellis, Chris Langridge make badminton semi-finals